Towards a balanced view of the bacterial tree of life
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Summary
A snapshot of bacterial phylogenetic diversity based on the recovery of high-quality SSU rRNA gene sequences extracted from nearly 7000 metagenomes and all available reference genomes is presented, providing a revised framework for future phylogeny-driven sequencing efforts.
- Type
- article
- Published
- 2017-10-17
- Cited by
- 110
- References
- 23
- Access
- Open access
- OpenAlex
- https://openalex.org/W2765982989
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:34435742
Keywords
Biology, Phylum, Metagenomics, Phylogenetic tree, Tree of life (biology)
References
- RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
- Unusual biology across a group comprising more than 15% of domain Bacteria
- Fermentation, Hydrogen, and Sulfur Metabolism in Multiple Uncultivated Bacterial Phyla
- Phylogeny of Bacterial and Archaeal Genomes Using Conserved Genes: Supertrees and Supermatrices
- FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments
- The SILVA ribosomal RNA gene database project: improved data processing and web-based tools
- A Simple and Accurate Method for Rogue Taxon Identification
- Integrating metagenomic and amplicon databases to resolve the phylogenetic and ecological diversity of the Chlamydiae
- Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses.
- Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample
- PrimerProspector: de novo design and taxonomic analysis of barcoded polymerase chain reaction primers
- Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons.
- Rfam 12.0: updates to the RNA families database
- Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences
- Infernal 1.1: 100-fold faster RNA homology searches
- Insights into the phylogeny and coding potential of microbial dark matter
- A new view of the tree of life
- Metagenomics uncovers gaps in amplicon-based detection of microbial diversity
- Status of the Archaeal and Bacterial Census: an Update
- IMG/M: integrated genome and metagenome comparative data analysis system
Cited by
- Meiosis: The Origins of Bias
- Microbial Biodiversity: Straight from the Dolphin's Mouth.
- Evolution of Phototrophy in the Chloroflexi Phylum Driven by Horizontal Gene Transfer
- A proposal for a standardized bacterial taxonomy based on genome phylogeny
- Major New Microbial Groups Expand Diversity and Alter our Understanding of the Tree of Life.
- On the maverick Planctomycetes
- A Network Science Approach for Determining the Ancestral Phylum of Bacteria
- A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life
- Candidate Phyla Radiation Roizmanbacteria from hot springs have novel, unexpectedly abundant, and potentially alternatively functioning CRISPR-Cas systems
- Mikrobaközösségek metabolikus aktivitása és 16S rRNS gén alapú filogenetikai diverzitása kukorica monokultúra rizoszféra-talajban
- phyloFlash – Rapid SSU rRNA profiling and targeted assembly from metagenomes
- A census-based estimate of Earth's bacterial and archaeal diversity
- Marine sediments illuminate Chlamydiae diversity and evolution
- Lignocellulolytic systems of soil bacteria: A vast and diverse toolbox for biotechnological conversion processes.
- The planktonic protist interactome: where do we stand after a century of research?
- Candidate Phyla Radiation Roizmanbacteria From Hot Springs Have Novel and Unexpectedly Abundant CRISPR-Cas Systems
- Current phylogeny of Rhodospirillaceae: a multi-approach study.
- Utilising genomics of novel uncultivable Chlamydiae to further understand chlamydial diversity, pathogenesis and evolution
- Phylogenomic analysis of 589 metagenome-assembled genomes encompassing all major prokaryotic lineages from the gut of higher termites
- Structure of a Synthetic β-Carboxysome Shell1[OPEN]
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